Didn't it have something to do with previously free foundry character slot being restricted to foundry characters only now? I bought 2x2 character slots with dilithium last month and only got 3 new slots.

Yeah, the Foundry granted a slot to Gold players, which many ended up using for a character rather then a Foundry Mission. When you become Silver you are supposed to lose that slot. If you deleted a character which used that slot then it is probably gone forever.